BowtieToBedFormat.jar from Vancouver Short Read Analysis Package

DrD2009 · 12-10-2009, 08:41 AM

Hello everyone,

I've been having problems using the BowtieToBedFormat tool that comes with the Vancouver Short Read Analysis Package. I have bowtie files in the default output and when I go to process them with the conversion tool it produces the output files:

Histogram.txt
log file
unpaired.tsv.gz
_simple_paired_samechr.tsv.gz
_simple_paired_spanchr.tsv.gz
_forked_paired.tsv.gz
_complex_paired.tsv.gz

Great right? Well, when I unzip the files they contain nothing or txt files that are blank.

Any suggestions? All I want to do is create a GFF or 3-column BED file from the bowtie output.

Thanks in advance,
Brandon

frozenlyse · 12-12-2009, 08:15 PM

you can use awk to turn a bowtie text output file into a 3 column bed file

Code:

awk -v bp=36 '{print $3"\t"$4"\t"($4+bp)}' infile.map > outfile.bed

set bp to however long your reads are, in this case 36bp
cheers

DrD2009 · 12-14-2009, 08:39 AM

:O It works!! Haha.

I had to learn what awk was, but after that I installed it on my Debian box and it worked perfectly.

Is there a way for it to work for sequence length ranges? I do have a couple bowtie files where all of the sequence lengths are 17, but there are a few where the lengths range 15-26bps, is there a setting for that using awk?

Thank you so much.

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12-10-2009, 08:41 AM	#1
DrD2009 Member Location: Kansas City Join Date: Oct 2009 Posts: 88	BowtieToBedFormat.jar from Vancouver Short Read Analysis Package Hello everyone, I've been having problems using the BowtieToBedFormat tool that comes with the Vancouver Short Read Analysis Package. I have bowtie files in the default output and when I go to process them with the conversion tool it produces the output files: Histogram.txt log file unpaired.tsv.gz _simple_paired_samechr.tsv.gz _simple_paired_spanchr.tsv.gz _forked_paired.tsv.gz _complex_paired.tsv.gz Great right? Well, when I unzip the files they contain nothing or txt files that are blank. Any suggestions? All I want to do is create a GFF or 3-column BED file from the bowtie output. Thanks in advance, Brandon

12-12-2009, 08:15 PM	#2
frozenlyse Senior Member Location: Australia Join Date: Sep 2008 Posts: 136	you can use awk to turn a bowtie text output file into a 3 column bed file Code: awk -v bp=36 '{print $3"\t"$4"\t"($4+bp)}' infile.map > outfile.bed set bp to however long your reads are, in this case 36bp cheers

12-14-2009, 08:39 AM	#3
DrD2009 Member Location: Kansas City Join Date: Oct 2009 Posts: 88	:O It works!! Haha. I had to learn what awk was, but after that I installed it on my Debian box and it worked perfectly. Is there a way for it to work for sequence length ranges? I do have a couple bowtie files where all of the sequence lengths are 17, but there are a few where the lengths range 15-26bps, is there a setting for that using awk? Thank you so much.